› 4apq

X-ray diffraction
3Å resolution

Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-sulfatide

Released:
DOI: 10.2210/pdb4apq/pdb
PDB entry 4apq coloured by chain, front view.
PDB entry 4apq coloured by chain, side view.
PDB entry 4apq coloured by chain, top view.
Source organism: Mus musculus
Entry authors: Clarke AJ, Le Nours J, Rossjohn J

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-208576 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (7 distinct):
Antigen-presenting glycoprotein CD1d1 Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 34.66 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P11609 (Residues: 19-297; Coverage: 88%)
Gene names: Cd1.1, Cd1d1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
T cell receptor alpha chain constant Chain: C
Molecule details ›
Chain: C
Length: 207 amino acids
Theoretical weight: 22.78 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC
Sequence domains: Domain of unknown function (DUF1968)
Structure domains: Immunoglobulins
MOUSE NKT TCR AUTOREACTIVE-VBETA6, HUMAN NKT TCR AUTOREACTIVE-VBETA6 Chain: D
Molecule details ›
Chain: D
Length: 243 amino acids
Theoretical weight: 27.37 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
1 bound ligand:
Ligand CIS 1 x CIS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P41212
Unit cell:
a: 95.11Å b: 95.11Å c: 291.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.232
Expression systems:
  • Trichoplusia ni
  • Escherichia coli BL21(DE3)

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